[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference
[2023-03-19 02:05:13,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,264] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,264] [INFO] Running command: cat /var/lib/cwl/stg028b316c-3ba9-472a-9910-8e256132cf28/OceanDNA-b322.fa | prodigal -d OceanDNA-b322/cds.fna -a OceanDNA-b322/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:19,399] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:19,399] [INFO] Task started: HMMsearch
[2023-03-19 02:05:19,399] [INFO] Running command: hmmsearch --tblout OceanDNA-b322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/reference_markers.hmm OceanDNA-b322/protein.faa > /dev/null
[2023-03-19 02:05:19,547] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:19,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg028b316c-3ba9-472a-9910-8e256132cf28/OceanDNA-b322.fa]
[2023-03-19 02:05:19,560] [INFO] Query marker FASTA was written to OceanDNA-b322/markers.fasta
[2023-03-19 02:05:19,560] [INFO] Task started: Blastn
[2023-03-19 02:05:19,560] [INFO] Running command: blastn -query OceanDNA-b322/markers.fasta -db /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/reference_markers.fasta -out OceanDNA-b322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:20,091] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:20,092] [INFO] Selected 14 target genomes.
[2023-03-19 02:05:20,092] [INFO] Target genome list was writen to OceanDNA-b322/target_genomes.txt
[2023-03-19 02:05:20,102] [INFO] Task started: fastANI
[2023-03-19 02:05:20,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg028b316c-3ba9-472a-9910-8e256132cf28/OceanDNA-b322.fa --refList OceanDNA-b322/target_genomes.txt --output OceanDNA-b322/fastani_result.tsv --threads 1
[2023-03-19 02:05:26,668] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:26,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:26,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:26,669] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:26,669] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:26,669] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-19 02:05:26,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b322/tc_result.tsv
[2023-03-19 02:05:26,670] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:26,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:26,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/checkm_data
[2023-03-19 02:05:26,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:26,677] [INFO] Task started: CheckM
[2023-03-19 02:05:26,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b322/checkm_input OceanDNA-b322/checkm_result
[2023-03-19 02:05:47,482] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:47,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:47,484] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:47,484] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:47,484] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b322/markers.fasta)
[2023-03-19 02:05:47,486] [INFO] Task started: Blastn
[2023-03-19 02:05:47,486] [INFO] Running command: blastn -query OceanDNA-b322/markers.fasta -db /var/lib/cwl/stg69b5d31d-9f61-4ad5-8530-8a0ae046b1c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:48,134] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:48,135] [INFO] Selected 20 target genomes.
[2023-03-19 02:05:48,135] [INFO] Target genome list was writen to OceanDNA-b322/target_genomes_gtdb.txt
[2023-03-19 02:05:48,403] [INFO] Task started: fastANI
[2023-03-19 02:05:48,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg028b316c-3ba9-472a-9910-8e256132cf28/OceanDNA-b322.fa --refList OceanDNA-b322/target_genomes_gtdb.txt --output OceanDNA-b322/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:05:56,885] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:56,887] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:05:56,887] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_009694435.1	s__SHUY01 sp009694435	97.4514	294	323	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__SHUY01	95.0	97.29	97.00	0.88	0.86	7	conclusive
--------------------------------------------------------------------------------
[2023-03-19 02:05:56,887] [INFO] GTDB search result was written to OceanDNA-b322/result_gtdb.tsv
[2023-03-19 02:05:56,887] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:05:56,887] [INFO] DFAST_QC result json was written to OceanDNA-b322/dqc_result.json
[2023-03-19 02:05:56,888] [INFO] DFAST_QC completed!
[2023-03-19 02:05:56,888] [INFO] Total running time: 0h0m45s